IMP logo
IMP Reference Guide  develop.27926d84dc,2024/04/19
The Integrative Modeling Platform
version 20240419.develop.27926d84dc
atom/cg_pdb.py

This example shows how to properly write out a pdb of the structure results when using coarse grained rigid bodies.

1 ## \example atom/cg_pdb.py
2 # This example shows how to properly write out a pdb of the structure
3 # results when using coarse grained rigid bodies.
4 
5 from __future__ import print_function
6 import IMP.atom
7 import sys
8 
9 IMP.setup_from_argv(sys.argv, "CG pdb")
10 
11 m = IMP.Model()
12 full = IMP.atom.read_pdb(IMP.atom.get_example_path("example_protein.pdb"), m)
13 chain = IMP.atom.get_by_type(full, IMP.atom.CHAIN_TYPE)[0]
14 print(chain)
15 # for some reason the Python wrapper won't make the implicit conversion to
16 # Chain
17 simplified = IMP.atom.create_simplified_along_backbone(
18  IMP.atom.Chain(chain), 3)
19 IMP.atom.destroy(full)
20 rb = IMP.atom.create_rigid_body(simplified)
21 original_transform = rb.get_reference_frame().get_transformation_to()
22 
23 
24 # fake optimization, just move the rigid body
25 tr = IMP.algebra.get_random_rotation_3d()
26 rb.set_reference_frame(IMP.algebra.ReferenceFrame3D(
27  IMP.algebra.Transformation3D(tr, IMP.algebra.Vector3D(0, 0, 0))))
28 
29 # extract the difference
30 diff = rb.get_reference_frame().get_transformation_to() / original_transform
31 reload = IMP.atom.read_pdb(IMP.atom.get_example_path("example_protein.pdb"), m)
32 IMP.atom.transform(reload, diff)
33 name = IMP.create_temporary_file("out", ".pdb")
34 IMP.atom.write_pdb(reload, name)